Estimation of the rate of physiological processes of planktonic microorganisms in natural waters is plagued by a question common to all areas of experimental science. Does the act of observing change that which is observed? Enclosure and incubation of natural communities in bottles can, at least in some instances, cause profound changes in community structure. It has been found that phytoplankton species abundances declined by an average of about 20% during 12 to 24 hour incubations in 250 ml bottles. Some protozooplankton groups dissappeared completely and chrophyll and ATP declined 10 to 30%. Other researchers have reported abnormally high rates of photochemical pigment destruction during incubation, which varied inversely with bottle volume. If bottle confinement or sample handling is responsible for such die offs in 12 to 24 hour periods, there must be an even more profound and rapid degradation of the physiological condition of the population.
As an alternative to bottle incubation methods, information on total system metabolism can be obtained from determinatins of plankton biomass and chemical parameters, such as organic and inorganic nutrients, dissolved O.sub.2 and total CO.sub.2, on samples taken directly from the natural environment at intervals over diel periods. This approach avoids the uncertainties of bottle incubation; however, in open water studies, advective and mixing processes cloud the interpretation of the results irregardless of what precautions are applied. In addition, free water studies usually preclude the use of radiotracers for physiological rate measurements.